Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Salma Salhi
Sent: Sunday, May 22, 2022 10:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_surf2surf error: No such file or directory (but file
exists)
External Email - Use Caution
Hello FreeSurfer De
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to run the mri_surf2surf command as shown in this MRtrix tutorial
on page 35
(https://secure-web.cisco.com/1IRfOd9DbtoZ73ePUy1kNxDjehQaayodvb_Pq3LttY1M2YqbKQhQ1UWIVGQmivIOeHqfZlJkiIPiENR9fGdSkObi00qtpoSZ8Jm9ww
22 10:42 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_surf2surf error
That mgh file has nothing in it (all dimensions 0). How did you create it?
On 5/12/2022 5:20 PM, Zhang, Fan wrote:
*External Email - Use Caution *
Hi Dr. Greve,
I got this when
the “load_mgh” in MATLAB and it showed the dimension is [10242, 1, 1, 78].
Thanks,
Fan
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Thursday, May 12, 2022 10:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_surf2surf error
That mgh file
It looks like you stopped the job and restarted it. Is that correct? If
so, I think something might have gotten out of sync. If you did not make
any edits (eg, to correct the defects), then can you start it from scratch?
On 5/12/2022 4:29 PM, Margot Wagner wrote:
External Email - Use
:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_surf2surf error
what happens if you run
mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh
On 5/3/2022 11:54 AM, Zhang, Fan wrote:
External Email - Use Caution
Hello Everyone,
I am trying to run mri_surf2surf. But I got some
-0. -0. -0. 1.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Thursday, May 5, 2022 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_surf2surf error
what happens if you run
what happens if you run
mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh
On 5/3/2022 11:54 AM, Zhang, Fan wrote:
External Email - Use Caution
Hello Everyone,
I am trying to run mri_surf2surf. But I got some errors saying "no
such file or directory" while in fact there are files in
External Email - Use Caution
Hello Everyone,
I am trying to run mri_surf2surf. But I got some errors saying "no such file or
directory" while in fact there are files in the pathway. I was able to run this
previously, so I am not sure if this is relevant to the recent upgrade of
This is because it takes two passes through the transform. One takes
each target vertex and finds the closest source vertex. The other takes
each source vertex not already sampled and finds the closest target
vertex to make sure that every source is represented. With the 2nd step,
there may be
External Email - Use Caution
Hi experts,
I am trying to resample some surface overlays from fsaverage to fsaverage_sym
surface. I have used the following command:
mri_surf2surf --srcsubject fsaverage --srcsurfreg fsaverage_sym.sphere.reg
--trgsubject fsaverage_sym --trgsurfreg
Can you give the command line that is failing and the terminal output?
On 3/4/2021 12:53 AM, 1248742467 wrote:
?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
Hello, Fs
I want to template some subject to fsaverage5, but now I meet some
problems
FreeSurfer version: Fs6
Download
External Email - Use Caution
Hello, Fs
I want to template some subject to fsaverage5, but now I meet some problems
FreeSurfer version: Fs6
Download the files: HLN-12-2.tar.gz OASIS-TRT-20-1.tar.gz
Twins-2-1.tar.gz Twins-2-2.tar.gz(https://secure-web.cisco.com/1yywjdkihIUyeuY
It looks like you edited the subject but did not fully re-run it. Try
recon-all -s HLN-12-2 -autorecon3
On 12/1/2020 4:01 AM, 1248742467 wrote:
External Email - Use Caution
Hello, Fs
When I run the following command:
mri_surf2surf --srcsubject HLN-12-2 --sval area --src_type curv --trg
External Email - Use Caution
Hello, Fs
When I run the following command:
mri_surf2surf --srcsubject HLN-12-2 --sval area --src_type curv --trgsubject
fsaverage5 --trgsurfval
/home/tj/application/freesurfer/subjects/min_template/HLN-12-2-target/area
--trg_type curv --hemi lh
How was lh.sphere.reg created? It might be corrupted, so try creating it again.
On 11/30/2020 3:11 AM, 1248742467 wrote:
External Email - Use Caution
Hello,Fs
When I used mri_surf2surf command to template the lh.thickness to fsaverage5
space, the error appeared:
Command:
mri_surf2surf -
External Email - Use Caution
Hello,Fs
When I used mri_surf2surf command to template the lh.thickness to fsaverage5
space, the error appeared:
Command:
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval thickness --src_type curv
--trgsubject fsaverage5 --trgsurfval
/home/tj/applica
I think that would be ok, but I would run this instead
mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type
curv --cortex --trgsubject fsaverage5 --trgsurfval ./mgh/1001_lh_fs5_thick.mgh
--trg_type mgh –fwhm-trg 10
On 11/23/2020 4:11 PM, Daniel Leopold wrote:
External Email - Use Caution
Dear Freesurfer experts,
The mri_surf2surf example 1 specifies that lh thickness is resampled onto
the 7th order icosahedron. Does it place the lh.thickness curv into
freesurfer space, or is it still in the subject's native space (i.e.,
pre-transformat
Dont use --trgicoorder. Also, smooth the input, not the output (ie, use
--fwhm not --fwhm-trg). Don't use projfrac there (which will fix the
--sval-xyz error). Your 2nd command looks the same as the first
On 9/27/20 10:30 PM, 谢娆 wrote:
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Hi,
To begin with,
External Email - Use Caution
Hi,
To begin with, I want clarify my goal here: I want to resample my resting-state
functional data in fsaverage5 and then do some preprocessing before statistical
analysis, and I get stuck in smooth now.
I tried the following command:
mri_surf2sur
run mri_surf2surf with --help and see example 3
On 9/16/2020 9:01 PM, 1248742467 wrote:
External Email - Use Caution
hello,Fs
Because I want to build an N*N matrix based on the fixed-point number
N of rh.white, but the original rh.white has too many fixed-point
numbers, a memory er
External Email - Use Caution
hello,Fs
Because I want to build an N*N matrix based on the fixed-point number N of
rh.white, but the original rh.white has too many fixed-point numbers, a memory
error occurs. I saw a paper, which can be registered to the fsaverage5 space,
and t
External Email - Use Caution
Thanks Doug, that worked! Caspar
Am Di., 3. Sept. 2019 um 17:03 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:
> Yes, just specify --surfreg white (or some other surface you do have).
>
> On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik wrot
Yes, just specify --surfreg white (or some other surface you do have).
On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik wrote:
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Hi!
I am having some issues projecting retinotopic mapping data from a monkey
analyzed in surface space onto its surface using rtview. Th
External Email - Use Caution
Hi!
I am having some issues projecting retinotopic mapping data from a monkey
analyzed in surface space onto its surface using rtview. The issue seems to
be that the data need to be converted into paint format through
mri_surf2surf, and that we do not h
From: Larson, Kathleen E
Sent: Tuesday, April 16, 2019 2:15 PM
To: Freesurfer support list
Subject: RE: [Freesurfer] mri_surf2surf help
Thank you! Yes, I was able to figure it out. However, even when I swap the
moving/target inputs, the surface is still not in the correct
boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D.
> [dgr...@mgh.harvard.edu]
> Sent: Thursday, April 11, 2019 10:37 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_surf2surf help
>
> You are almost there. You need to swap mov and targ in your tk
u] on behalf of Greve, Douglas N.,Ph.D.
[dgr...@mgh.harvard.edu]
Sent: Thursday, April 11, 2019 10:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_surf2surf help
You are almost there. You need to swap mov and targ in your tkregister2
command. I also found these instructio
08, 2019 12:27 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_surf2surf help
>
> Have you looked at the help? Run with --help and look at example 4
> doug
>
> On 4/4/19 9:56 PM, Larson, Kathleen E wrote:
>> External Email - Use Caution
>&
Katie
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D.
[dgr...@mgh.harvard.edu]
Sent: Monday, April 08, 2019 12:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_surf
Have you looked at the help? Run with --help and look at example 4
doug
On 4/4/19 9:56 PM, Larson, Kathleen E wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer developers,
>
> I'm having trouble running the command mri_surf2surf, and I haven't
> been able to find a fix in the m
External Email - Use Caution
Hello FreeSurfer developers,
I'm having trouble running the command mri_surf2surf, and I haven't been able
to find a fix in the message archives (a similar question has been asked, but I
couldn't find the answer). I am trying to convert the pial and
Hi Stephanie
I guess visually. You can write a script to run freeview and save a
snapshot using something like:
foreach s ($SUBJECTS)
freeview -f ... -ss then you can zip through them in nmovie (or nmovie_qt, which I guess is
what we support now)
cheers
Bruce
On Fri, 15 Feb 2019, Winkel
External Email - Use Caution
Hi Freesurfers,
I ran mri_surf2surf and registered self-created parcels from fsaverage to all
my subjects. What is the best way to do QC and check if everything went right?
Thanks for your help!
Stephanie
The information contained in this electron
Ok, thanks, that was very helpful. It was the surf2surf_nnfr() call that made
me suspicious. And as you say, when run without specifying —mapmethod (sets the
map method to nnfr in default) it gives out the surf2surf:Reverse Loop
statement.
Thanks
Olivia
On 3 Oct 2018, at 23:31, Greve, Douglas
Are you worried about where it says "Using surf2surf_nnfr()"? There is actually
one one function that performs both kinds of mapping. In this case, it is not
doing the reverse loop. You can reassure yourself by running it with nnfr and
see that it prints out "Surf2Surf: Reverse Loop" (which does
Hello,
I am using mri_surf2surf and would like to use the vertex map method nnf
("neighest neighbor, forward only") which according to the --help description
exists and avoids multiple source vertices to be mapped and averaged onto a
single target vertex (crucial to my analysis here). However,
can you send your command line and terminal output?
On 04/11/2018 05:41 AM, Frauke Beyer wrote:
> Dear experts,
>
> I have an issue with mri_surf2surf (i suspect). I have resampled
> T1-values to the fsaverage template using mri_vol2surf and a --projfrac
> of 0.25 with the default white matter su
Dear experts,
I have an issue with mri_surf2surf (i suspect). I have resampled
T1-values to the fsaverage template using mri_vol2surf and a --projfrac
of 0.25 with the default white matter surface. Then I loaded these
values in Matlab using MRIread, inverted them and saved them back into a
file us
Can you send the terminal output? Also, can you check the number of
vertices in the xhemi folder and make sure that the lh in the xhemi
matches the rh in the main folder?
On 12/13/2017 05:13 PM, Defenderfer, Matthew K wrote:
>
> Hi all,
>
>
> I am trying to transfer a surface file from fsavera
: Wednesday, December 13, 2017 4:16:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_surf2surf on edited subjects
Hi Matt
can you run mris_euler_number on that subject's lh.sphere.reg and see if it
has the same number of vertices as the lh.pial for example? Or check
timestamps.
Hi Matt
can you run mris_euler_number on that subject's lh.sphere.reg and see if it
has the same number of vertices as the lh.pial for example? Or check
timestamps. If it was not recreated after your editing you will need to
rerun part of recon-all
cheers
Bruce
On
Wed, 13 Dec 2017, Defend
Hi all,
I am trying to transfer a surface file from fsaverage_sym space to a recently
edited individual subject's hemisphere. I previously ran recon-all on the
subject and then edited the wm, brainmask, etc. to fix some defects I had
found. Before the edits, I could transfer the surface and lo
Hi Doug,
Thanks very much for your reply.
The mri_vol2surf command line i used is:
mri_vol2surf --mov brainmask.nii.gz --reg bbregister.dof6.dat --trgsubject
fsaverage --interp trilin --projfrac 0.5 --hemi ${hemi} --o
brainmask.fsaverage.${hemi}.nii.gz --noreshape --cortex --surfreg sphere.reg
Hi dong, sorry for the delay. What is your mri_vol2surf command line?
On 10/20/17 4:44 AM, Dongnandi wrote:
Dear Freesurfer experts,
I have a binary brainmask made in volumetric space and trying to
transfer it into surface space, first I use mri_vol2surf to transfer
the mask into fsaverage
Dear Freesurfer experts,
I have a binary brainmask made in volumetric space and trying to transfer it
into surface space, first I use mri_vol2surf to transfer the mask into
fsaverage space, then run mri_surf2surf (fs 6.0) to down sample it to
fsaverage5 space.
After vol2surf, some values
On 03/06/2016 08:23 PM, marmaduke woodman wrote:
> mri_surf2surf ...--tval-xyz ./tvb/mri/T1.mgz
just to follow up, it seems --tval-xyz is a flag (no argument) on
stable, but on dev takes an argument.
So, on stable, just
mri_surf2surf ... --tval-xyz
will run, but the resulting surface doesn't
Hi
The command
mri_surf2surf --srcsubject tvb --trgsubject fsaverage5 --hemi lh
--sval-xyz pial --tval pial.tvb --tval-xyz ./tvb/mri/T1.mgz
works on dev (mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve), but on
stable fails with
ERROR: Option ./tvb/mri/T1.mgz unknown
Is there a simple wor
as long as it is the same subject/hemi, then yes
On Tue, 10 Nov 2015, Gardus
III, John D wrote:
> Hi Bruce and Doug,
>
> Thanks so much for the advice.
>
> I think I'll try to hack something together since I have to perform this
> step for numerous subjects.
>
> One quick question - is the order
Yes, the order is preserved.
On 11/10/2015 11:05 AM, Gardus III, John D wrote:
> Hi Bruce and Doug,
>
> Thanks so much for the advice.
>
> I think I'll try to hack something together since I have to perform this
> step for numerous subjects.
>
> One quick question - is the order of the vertices pr
Hi Bruce and Doug,
Thanks so much for the advice.
I think I'll try to hack something together since I have to perform this
step for numerous subjects.
One quick question - is the order of the vertices preserved between the
pial curv and spherical curv ascii files?
Thanks again,
John
On 11/9/1
there used to be something built into tksurfer to do soap bubble
smoothing. You can try smooth_vals_spare from the tcl prompt. I think it
depends on setting the fixedval field in the vertex struct to 1 for the
stationary points of the soap bubble. You can first read in a file that is
1 for the
Sounds like you are trying to do soap bubble interpolation (?). I don't
think we have a binary for that. Maybe Bruce knows of one. You could
hack something together, with smoothing (mri_surf2surf), creating binary
masks (mris_binarize), and masking (mri_mask), and basic math operations
(fscalc
Hello all,
I'm in the process of mapping some non-FreeSurfer derived outcomes to a curv
file containing the vertices of the pial surface mesh. I have values at roughly
100 vertices, leaving some 37000 with 'nan'.
I then run an intra-subject surf2surf command in an attempt to interpolate
betwee
You can't use analyze for this. mgh format will work. nii might work
On 05/13/2014 04:37 AM, Caka wrote:
> Dear Doug and All,
>
> I want to register the individual subject surface into the fsaverage surface.
> I used mdi_surf2surf command. But one error occurred. Could you please help
> me with
Hi Qiongmin
try making the output format .mgz (or maybe .nii) and see if that fixes the
problem
cheers
Bruce
On Tue, 13 May 2014, Caka wrote:
Dear Doug and All,
I want to register the individual subject surface into the fsaverage surface. I
used mdi_surf2surf command. But one error occur
Dear Doug and All,
I want to register the individual subject surface into the fsaverage surface. I
used mdi_surf2surf command. But one error occurred. Could you please help me
with this. Here are the scripts:
—
[root@localhost sub001]# mr
That worked like a charm.
Thanks!
On Wed, Oct 23, 2013 at 5:14 PM, Bruce Fischl wrote:
> try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of
> --srcsurfval
>
> cheers
> Bruce
>
> On Wed, 23 Oct 2013, Paul Beach wrote:
>
> Apologies: the full error message was: 'could not det
try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of
--srcsurfval
cheers
Bruce
On Wed, 23 Oct 2013, Paul Beach wrote:
Apologies: the full error message was: 'could not determine type of
lh.Yeo2011_17Networks_N1000.annot'
I tried your suggestion of removing the hemispheric des
Apologies: the full error message was:
'*could not determine type of lh.Yeo2011_17Networks_N1000.annot*'
I tried your suggestion of removing the hemispheric designation in front of
'Yeo' and I'm getting the same error - - the same occurs if I remove the
'.annot' at the end.
*mri_surf2surf --srcsu
The full error msg is not in the subject line. My guess is that the
"lh." in front of "Yeo" in the srcsurfval is causing the problem
On 10/23/2013 03:17 PM, Paul Beach wrote:
> Hello FS experts,
>
> I'm attempting to transform the Yeo2011 annotations (lh & rh) from
> fsaverage to individual su
Hello FS experts,
I'm attempting to transform the Yeo2011 annotations (lh & rh) from
fsaverage to individual subjects so as to then sample the cortical maps to
subject surfaces using mri_label2vol. However, I'm getting the error in the
subject line when I put in the following commands:
*mri_surf2
Hi Doug,
I found a workaround. I used matlab code from from gradient_nonlin_unwarp to
remove the c_ras offset from the vertex coordinates and set c_ras to 0. Then I
mris_convert the new surface to .gii. This gives me perfectly aligned surfaces.
Thanks for your help,
Franz
> [surf_struct, tags,
This info is probably not stored in the gii header. I'll have to take a
look which could take a while. Depending on what you are doing, it might
not be important.
doug
On 9/2/13 2:58 PM, Franz Liem wrote:
> Hi Doug,
> this gives exactly the same surface as surf2surf followed by mris_convert
>
Hi Doug,
this gives exactly the same surface as surf2surf followed by mris_convert (i.e.
with offset).
Thanks,
Franz
Am 02.09.2013 um 16:50 schrieb Douglas Greve:
>
> What if you specify the output of surf2surf to be a gii file?
>
>
> On 9/2/13 6:47 AM, Franz Liem wrote:
>> Dear Doug,
>>
>>
What if you specify the output of surf2surf to be a gii file?
On 9/2/13 6:47 AM, Franz Liem wrote:
> Dear Doug,
>
> thank you so much, the fix works great.
> The problem now is that when I mris_convert the newly generated surface to
> .gii the volume geometry is lost again and the offset reintr
Dear Doug,
thank you so much, the fix works great.
The problem now is that when I mris_convert the newly generated surface to .gii
the volume geometry is lost again and the offset reintroduced.
Is there a way to fix this? I have tried to give mri_surf2surf a register.dat
that would correct for
Sorry, I'm answering your emails in reverse order. Your command should
do what youwant once you use the new version below
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard
note the --tval-xyz requires an argument (give it the orig.mgz)
doug
On 08/30/2013
Oh, I see. It must be the volume geometry being invalid. When I try it
with the new version of mri_surf2surf, the two surfaces are right on top
of each other.
doug
On 08/30/2013 09:22 AM, Franz Liem wrote:
> Hi again,
> just a clarification. The two surfaces in the image are single subject
>
Hi again,
just a clarification. The two surfaces in the image are single subject surfaces
(the original lh.white and the transformed lh.white.ico6), not fsaverage6
surfs.
Best,
Franz
Am 30.08.2013 um 09:51 schrieb Franz Liem:
> Hi Doug,
>
> thanks a lot.
> I am using Darwin-snowleopard and c
Hi Doug,
thanks a lot.
I am using Darwin-snowleopard and centos6_x86_64.
What I am trying to do is to use the white surface as seed for probtrackx.
Therefore, I would like to reduce the number of vertices and at the same time
bring the surfaces into a common space (so that vertex x is meaning
Hi Franz, I just programmed a fix into mri_surf2surf. What platform do
you use?
As for the shift, you would not expect them to line up. In fact, that
command line does not make a lot of sense. What it is doing is mapping
the xyz coordinates in the native space to a new tesselation. The xyz
co
Dear Freesurfers,
sorry for the bump, but my message seems to have gone unnoticed.
Thanks so much for any ideas.
Franz
Am 22.08.2013 um 13:37 schrieb Franz Liem:
> Dear Freesurfers,
>
> I tried to map a single subject surface to fsaverageX (for the sake of
> demonstration lets take fsaverage6)
Dear Freesurfers,
I tried to map a single subject surface to fsaverageX (for the sake of
demonstration lets take fsaverage6). I did the following:
mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject
fsaverage6 --tval-xyz --tval ./lh.white.ico6
This produces a surface that seems
Hi Zhu
what is your command line?
Bruce
On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote:
> Hi Freesurfers,
>
> I'm trying to extracting thickness value for a ROI which is created by afni.I
> follow the workflows of "Cortical Thickness of a Volume-defined ROI". The ROI
> mask and T1 volum
Hi Freesurfers,
I'm trying to extracting thickness value for a ROI which is created by afni.I
follow the workflows of "Cortical Thickness of a Volume-defined ROI". The ROI
mask and T1 volume file are all talairach transformed.
When I map the thickness data to the fsaverage subject with mri_surf
you probably need to redo them since it didn't find the cortex.label it
will include the zero thicknesses in the medial wall for example
On Fri, 1
Jun 2012, mdkrue...@uwalumni.com wrote:
Actually one last question-
I used label2label to transfer some labels and grab ROI thickness averages fro
I see. So you must have overwritten it with something, maybe a stats
file. You'll need to rerun mris_make_surfaces or autorecon 3 for that
subject/hemi to recreate it.
cheers
Bruce
On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
wrote:
> Bruce-
>
> It is, and i agree, for instance here is the lh.co
that makes sense. also just for clarification to a point a made before - i
was not using label2label to transfer the rh.cortex.label we have been
discussing across subjects, i was transferring other labels, which is most
likely why the label2label and measurements didnt fail. I believe i
misunderst
not unless you are trying to visualize the label
On 06/01/2012 01:16 PM, mdkrue...@uwalumni.com wrote:
> Thanks, i am also still able to display the rh in tksurfer without
> issue, shouldnt that also fail with the current rh.cortex.label?
>
> michael
>
> On Fri, Jun 1, 2012 at 11:57 AM, Douglas N
Thanks, i am also still able to display the rh in tksurfer without issue,
shouldnt that also fail with the current rh.cortex.label?
michael
On Fri, Jun 1, 2012 at 11:57 AM, Douglas N Greve
wrote:
> I would have expected that to fail. You can check the time stamps to see
> if your output is newer
I would have expected that to fail. You can check the time stamps to see
if your output is newer or older than rh.cortex.label. If older, it is
probably ok.
On 06/01/2012 12:53 PM, mdkrue...@uwalumni.com wrote:
> Actually one last question-
>
> I used label2label to transfer some labels and grab
Actually one last question-
I used label2label to transfer some labels and grab ROI thickness averages
from the labels on the subject with the rh.cortex.label that has been
overwritten. I received no errors during this, does this mean that the
label transfers and averages are valid, or do i need t
Doug -
That does indeed seem to be the problem! Ill just rerun some things here to
rectify that. Thanks for all the help everyone!
Best-
Michael
On Fri, Jun 1, 2012 at 11:01 AM, Douglas N Greve
wrote:
> I think the label file got overwritten at some point. Check the time
> stamp and see if it i
I think the label file got overwritten at some point. Check the time
stamp and see if it is much different than the other rh files
On 06/01/2012 11:55 AM, mdkrue...@uwalumni.com wrote:
> Bruce-
>
> It is, and i agree, for instance here is the lh.cortex.label file
>
> #label , from subject ??
> 14
Doug-
INPUT
mri_surf2surf --hemi rh --s UNM_SUPERSAMPLE --sval rh.meth.00.mgh
--fwhm 10 --cortex --tval rh.meth.10.mgh
OUTPUT
srcsubject = UNM_SUPERSAMPLE
srcval = rh.meth.00.mgh
srctype=
trgsubject = UNM_SUPERSAMPLE
trgval = rh.meth.10.mgh
trgtype=
srcsurfreg = sphere.reg
trgs
Bruce-
It is, and i agree, for instance here is the lh.cortex.label file
#label , from subject ??
149955
22 -10.374 55.016 3.203 0.00
112 -6.294 36.386 -7.809 0.00
114 -6.137 38.556 13.808 0.00
247 -11.304 45.214 -2.709 0.00
248 -6.278 39.973 2.192 0
what is your full command line and terminal output?
doug
On 06/01/2012 11:49 AM, Bruce Fischl wrote:
> that is the rh.cortex.label file? It doesn't look like it
>
> On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
> wrote:
>
>> Bruce-
>>
>> Here you go. Subjects recoded.
>>
>> Graph: name
>>
>> Dat
that is the rh.cortex.label file? It doesn't look like it
On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
wrote:
> Bruce-
>
> Here you go. Subjects recoded.
>
> Graph: name
>
> Data: path
> Variable: Subject
> Measurement: external
> subject id, class id, variable value, measurement value, stand
Bruce-
Here you go. Subjects recoded.
Graph: name
Data: path
Variable: Subject
Measurement: external
subject id, class id, variable value, measurement value, standard deviation
S1 Cl1 0.0 3.10522500831 0.268702566292
S2 Cl1 1.0 2.67585065105 0.396833961125
S3 Cl1 2.0 3.07631433273
Hi Michael
can you check to see that your partition is not full? Does the
rh.cortex.label file exist in that subject's label dir? If so, what are the
first couple of lines?
cheers
Bruce
On Fri, 1 Jun 2012,
mdkrue...@uwalumni.com wrote:
To anyone who can help -
I am trying to tun a GLM on
To anyone who can help -
I am trying to tun a GLM on a set of data and am currently receiving an
error during the mri_surf2surf portion. When running this portion i receive
an error ( could not scan # of lines from (path to rh.cortex.label)). This
does not happen when running this portion for the
hi doug,
thanks. we just wanted to verify that annot's are special. no need to hack
anything!
cheers,
satra
On Fri, May 25, 2012 at 11:27 AM, Douglas N Greve wrote:
> Currently, yes. If this is a burden for you, I could hack something.
> There might be other ways such as converting the annot
Currently, yes. If this is a burden for you, I could hack something.
There might be other ways such as converting the annot into a
segmentation (mris_annotation2label), passing that to surf2surf with
--sval (and --mapmethod nnf), then converting the output back to an
annotation (mris_seg2annot)
hi doug,
we are trying to figure out if for annot we *have to* use sval-annot or if
there is a way to do it with sval?
cheers,
satra
On Fri, May 25, 2012 at 9:46 AM, Douglas Greve wrote:
> If the source is an annot, then you need to use --sval-annot Is this
> causing a problem?
> doug
>
> On
If the source is an annot, then you need to use --sval-annot Is this
causing a problem?
doug
On 5/24/12 6:48 PM, Arno Klein wrote:
hello!
in mri_surf2surf, does anyone know how to specify the source and
target formats if --sval is annot without using --sval-annot, as in
"--sfmt" or "--tfmt"
hello!
in mri_surf2surf, does anyone know how to specify the source and target
formats if --sval is annot without using --sval-annot, as in "--sfmt" or
"--tfmt"?
cheers,
@rno
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not and keep the topology (there is some decimation that is used in the
EEG/MEG inverse stuff, but it's just to generate points, not faces)
On Fri,
9 Dec 2011, Douglas N Greve wrote:
> Bruce, do you have a command to reduce the number of vertices?
>
> John Griffiths wrote:
>>
>>
>> Ok. Can't s
it won't
On Fri, 9 Dec 2011, John Griffiths wrote:
Ok. Can't see any options in mris_smooth info reducing the number of vertices.
How would I do that?
Ta,
john
On 9 December 2011 17:22, Douglas N Greve wrote:
Yes, give it both --sval-xyz and --tval-xyz to indicate that t
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